|
| Status |
Public on Sep 14, 2017 |
| Title |
mg36 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organism |
Notamacropus eugenii |
| Characteristics |
age: day 36 of lactation
tissue: mammary gland
tissue state: fixed, 4% paraformaldehyde
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fixed samples were initially subjected to a brief protease digestion to remove nucleic acid cross-linking. Total RNA was then extracted using the ambion RecoverAll Total Nucleic Acid Isolation kit and mRNA was subsequently isolated using Dynabeads Oligo (dT)25.
the samples were given a short heat-shearing treatment immediately followed by cDNA synthesis. The resulting cDNA was repaired using 3’A-tailing and ligated to linkers containing unique illumina barcodes for sequencing. An agarose gel was used for size selection and the samples were then PCR amplified for 15(fresh)-17(fixed) cycles and purified using AMPure XP beads. Quality of the libraries was assessed using both Qubit and Bioanlyzer technology and then sequenced
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Adapter sequences and low quality bases were trimmed using trim_galore v 0.3.3
The resulting sequences were aligned to the wallaby genome (m.eug_v1.0) using STAR (version 2.5.1b).
Raw counts were assigned to significantly transcribed regions using UniPeak v1.0.
Regions were then associated with the nearest gene using HOMER (version 4.7)
Multiple regions mapping to the same gene were summed to give a final read count for each gene.
Genome_build: m.eug_v1.0
Supplementary_files_format_and_content: Tab-delimited file containing summed read counts for each transcript
|
| |
|
| Submission date |
Dec 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Warren Guernsey |
| E-mail(s) |
mikewg@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Genetics
|
| Lab |
Julie C. Baker
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18017 |
| Series (1) |
| GSE90838 |
Transcriptome sequencing in the tammar wallaby unveils conserved gene expression networks underlying reproduction in therian mammals |
|
| Relations |
| BioSample |
SAMN06106673 |
| SRA |
SRX2393523 |
